Mutated factor x polypeptides and uses thereof for the treatment of haemophilia

ABSTRACT

The present invention relates to mutated factor (FX) polypeptides and uses thereof for the treatment of haemophilia. In particular, the present invention relates to a mutated factor X (FX) polypeptide which comprises a heavy chain wherein at least one amino acid residue at position 401 or 408 is mutated.

FIELD OF THE INVENTION

The present invention relates to mutated factor (FX) polypeptides and uses thereof for the treatment of haemophilia.

BACKGROUND OF THE INVENTION

Haemophilia A and B are inherited X-linked coagulopathies characterized by a lack of coagulation factor VIII (FVIII) and factor IX (FIX) respectively. Haemophilia A affects about 1 in 5 000 and Haemophilia B about 1 in 35 000 male births (1,2). Haemophilia leads to impaired thrombin generation, weak and vulnerable clots, and therefore spontaneous bleeding. Compared to severe patients, bleeding episodes are less frequent in moderate/mild patients, and are usually provoked by trauma or invasive procedures. Current treatment includes replacement therapy with recombinant or purified FVIII or FIX (3). However, one of the most serious drawbacks of these treatments is the development of alloantibodies, called inhibitors, inhibiting the activity of the coagulation factor, in a non-negligible number of patients with haemophilia A: 20-25% of severe patients and 7-13% of moderate/mild patients (4). Treatment of these inhibitor patients is limited to FVIII- or IX-bypassing agents, such as recombinant FVIIa (Novoseven®) or plasma-derived activated prothrombin complex (FEIBA®). However, these products have considerably shorter half-lives (4-7 h for FEIBA® and 1.5-2.7 h for Novoseven®), than the respective half-lives of FVIII (˜12 h) and FIX (˜18 h). These short half-lives require the need for frequent infusions, limiting the use of both products for prophylactic purposes and increasing the costs. They are expensive and a substantial number of patients do not respond to these agents.

Therefore, alternative therapeutic approaches Factor X (FX) is a more attractive bypassing molecule, since it displays a ˜40 h half-life and is part of the coagulation cascade normally activated by both FVIII and FIX. For instance, a FX variant which combines activation of the molecule by thrombin with a long survival mimicking that of the FX zymogen was disclosed in WO 2010070137. This FX variant is activated without FVIII or FIX, in vitro as well as in vivo and could thus be used as a bypassing agent in both hemophilia A and B. However, the FX variants of the prior art are susceptible to inactivation due to the presence of inhibitors such as Antithrombin (AT) and/or the Tissue Pathway Inhibitor (TFPI). Actually, TFPI in complex with FXa (TFPI)-FXa inhibits the initiating complex of the coagulation Tissue Factor (TF)/FVIIa. TF/FVIIa complex initiates coagulation by activating FX. However, activation of FX to FXa by the FVIIIa/FIXa complex counteracts the activity of TFPI, allowing coagulation to proceed. In patients with haemophilia, the propagation phase of thrombin generation is not sustainable due to the lack of intrinsic tenase (FVIIIa/FIXa) complex (11). The limited availability of thrombin via TF-FVIIa pathway is in part due to rapid inhibition of FXa and thrombin by TFPI and AT (12, 13). In particular, plasma AT levels are normally high (2.6 μM), and AT is capable of inhibiting trace amounts of FXa and thrombin (13, 14). Therefore, a new upcoming strategy to treat coagulation disorders like hemophilia has recently emerged and implies neutralization of natural anticoagulants and especially TFPI and AT. This is based on several observations. Thus, low TFPI and AT levels in neonates are deemed to be important in augmenting thrombin generation with lower levels of procoagulant factors (15, 16). Furthermore, low AT levels improved haemostatic function in FVIII-deficient mice with heterozygous AT deficiency (17). Very recently, a biopharmaceutical company (Alnylam) developed an RNAi therapeutic targeting antithrombin (ALN-AT3) for the treatment of haemophilia and other rare bleeding disorders, which is currently being investigated in a multinational Phase 1 trial in haemophilia subjects. However, because of the high concentration of circulating plasma antithrombin (3-5 μM), targeting antithrombin via inhibitory molecules may not be the ideal way to obtain therapeutic attenuation of coagulation in haemophilia patients. For TFPI, different blocking reagents have been evaluated as possible therapeutic agents in different animal models with haemophilia (18, 19, 20, 21). However, there are some drawbacks for anti-TFPI agents. Indeed, TFPI is distributed among different pools: the major part is located in or at the endothelial surface, while the rest is distributed equally between platelets and plasma. Moreover, only 1% of total TFPI circulates as free protein in plasma, with the remainder bound to LDL-particles. Due to this complex biodistribution, it is difficult to monitor the efficacy of TFPI inhibition upon treatment in patient plasma samples. A second issue is that different splicing forms of TFPI are present (TFPIalpha and TFPIbeta), which act in different ways. Anti-TFPI based therapy should therefore be using agents that differentiate between both forms. To illustrate the difficulty to use the TFPI-blocking strategy, a clinical trial ran by Baxter using an aptamer directed against TFPI has been stopped due to an increased number of bleeding events. Biological explanations for this observation is that the blocking agent releases intracellularly stored TFPI, impacts its metabolism and prolongs its circulatory half-life.

SUMMARY OF THE INVENTION

The present invention relates to mutated factor (FX) polypeptides and uses thereof for the treatment of haemophilia. In particular, the present invention is defined by the claims.

DETAILED DESCRIPTION OF THE INVENTION

The inventors now describe new FX polypeptides in which at least one residue in the heavy chain were mutated at position 401 or 408 (FIG. 1). These selectively mutated residues on FX could thus interfere with the inhibition, when activated, by Antithrombin (AT) and/or the Tissue Pathway Inhibitor (TFPI). These properties give the proteins the potential to be used as bypassing agents in both haemophilia A and B, either episodically or prophylactically, and irrespective of the presence of inhibitors.

Accordingly a first object of the present invention relates to a mutated factor X (FX) polypeptide which comprises a heavy chain wherein at least one amino acid residue at position 401 or 408 is mutated.

As used herein, the term “Factor X” has its general meaning in the art and refers to a secreted serine protease implicated in coagulation mechanisms. The factor X can be from any source, but typically is a mammalian (e.g., human and non-human primate) factor X, and more particularly a human factor X. Typically, the amino acid sequence of the human factor X is provided by SEQ ID NO:1 (FIG. 1). There are different numbering systems to localize the amino acid residues for factor X: i) the system of numbering with reference of the sequence deduced from the cDNA of factor X (i.e. SEQ ID NO:1) and ii) the system of numbering with reference of the sequence deduced from the secreted protein, which contains the light chain, the activation peptide and the heavy chain wherein the amino acid residue numbered 1 is the first amino acid residue of the amino-terminal extremity of the light chain (FIG. 1). This numbering system is used in the present application. The amino acid position upstream are negatively identified: the C-terminal amino-acid of pro-peptide is numbered −1 and the N-terminal amino-acid residue of the translated protein (which is the amino-terminal amino acid residue of pre-peptide) is numbered −40. As shown in FIG. 1, the sequence of factor X is divided in five different regions, which correspond, according to the used numbering system to:

-   -   the pre-peptide (or signal peptide) between the positions −40 to         −28,     -   the pro-peptide between the positions −27 to −1,     -   the light chain between the positions 1 to 142     -   the activation peptide between the positions 143 to 194     -   the heavy chain between the position 195 to 448.

As used herein, the term “mature FX” or “zymogen FX” refers to the blood circulating form of factor X, after its secretion by the producing hepatic cells. The signal peptide is cleaved off by signal peptidase, the propeptide sequence is cleaved off after gamma carboxylation took place at the first 11 glutamic acid residues at the N-terminus of the mature N-terminal chain. A further processing step occurs by cleavage between Arg142 and Ser143 according to the used numbering system (FIG. 1, positions 182-183 of SEQ ID NO:1). This processing step also leads concomitantly to the deletion of the tripeptide Arg140-Lys141-Arg142 (positions 180-182 of SEQ ID NO:1). The resulting secreted factor X zymogen consists of an N-terminal light chain of 139 amino acids and a C-terminal heavy chain of 306 amino acids which are covalently linked via a disulfide bridge between Cys132 and Cys302. Further posttranslational processing steps include the beta-hydroxylation of Asp63 as well as N- and O-type glycosylation. The term “activated Factor X” or “FXa” thus refers to the enzymatically active form of circulating factor X generated in case of coagulation activity (e.g. thrombin generation) is needed. Under physiological conditions able to activate factor X, the so called activation peptide of 52 amino acids from Ser143 to Arg194 is cleaved off the rest of the molecule by cleaving carboxy-terminal end of the heavy chain at Arg194 (FIG. 1).

In some embodiments, the mutated FX polypeptide of the present invention comprises a heavy chain which consists of the amino acid sequence having at least 90% of identity with the sequence ranging from the amino acid residue at position 195 to the amino acid residue at position 448 wherein at least one amino acid residue at position 401 or 408 is mutated.

According to the invention a first amino acid sequence having at least 90% of identity with a second amino acid sequence means that the first sequence has 90; 91; 92; 93; 94; 95; 96; 97; 98; 99 or 100% of identity with the second amino acid sequence. Sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar are the two sequences. Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith and Waterman, Adv. Appl. Math., 2:482, 1981; Needleman and Wunsch, J. Mol. Biol., 48:443, 1970; Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A., 85:2444, 1988; Higgins and Sharp, Gene, 73:237-244, 1988; Higgins and Sharp, CABIOS, 5:151-153, 1989; Corpet et al. Nuc. Acids Res., 16:10881-10890, 1988; Huang et al., Comp. Appls Biosci., 8:155-165, 1992; and Pearson et al., Meth. Mol. Biol., 24:307-31, 1994). Altschul et al., Nat. Genet., 6:119-129, 1994, presents a detailed consideration of sequence alignment methods and homology calculations. By way of example, the alignment tools ALIGN (Myers and Miller, CABIOS 4:11-17, 1989) or LFASTA (Pearson and Lipman, 1988) may be used to perform sequence comparisons (Internet Program® 1996, W. R. Pearson and the University of Virginia, fasta20u63 version 2.0u63, release date December 1996). ALIGN compares entire sequences against one another, while LFASTA compares regions of local similarity. These alignment tools and their respective tutorials are available on the Internet at the NCSA Website, for instance. Alternatively, for comparisons of amino acid sequences of greater than about 30 amino acids, the Blast 2 sequences function can be employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11, and a per residue gap cost of 1). When aligning short peptides (fewer than around 30 amino acids), the alignment should be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). The BLAST sequence comparison system is available, for instance, from the NCBI web site; see also Altschul et al., J. Mol. Biol., 215:403-410, 1990; Gish. & States, Nature Genet., 3:266-272, 1993; Madden et al. Meth. Enzymol., 266:131-141, 1996; Altschul et al., Nucleic Acids Res., 25:3389-3402, 1997; and Zhang & Madden, Genome Res., 7:649-656, 1997.

In some embodiments, the mutated FX polypeptide of the invention comprises a heavy chain which consists of the amino acid sequence ranging from the amino acid residue at position 195 to the amino acid residue at position 448 wherein at least one amino acid residue at position 401 or 408 is mutated.

As used herein, the term “mutation” has its general meaning in the art and refers to a substitution, deletion or insertion. The term “substitution” means that a specific amino acid residue at a specific position is removed and another amino acid residue is inserted into the same position. The term “deletion” means that a specific amino acid residue is removed. The term “insertion” means that one or more amino acid residues are inserted before or after a specific amino acid residue, more specifically, that one or more, preferably one or several, amino acid residues are bound to an a.-carboxyl group or an a,-amino group of the specific amino acid residue.

In some embodiments, the residue at position 401 or 408 is substituted so that the side chain charge at pH=7,4 is reversed (e.g. negative to positive charge) or is rendered neutral (e.g. negative to neutral charge). In some embodiments, the weight and the hydropathy index remains in the same range.

In some embodiments, the glutamic acid residue (E) at position 401 is substituted by an amino acid residue selected from the group consisting of glutamine (Q), alanine (A), lysine (K) or arginine (R).

In some embodiments, the lysine residue (K) at position 408 is substituted by an amino acid residue selected from the group consisting of asparagine (N), alanine (A), glutamic acid (E) and aspartic acid (D).

In some embodiments, the mutated FX polypeptide of the present invention further comprises a fibrinopeptide A which is inserted between the activation peptide and the heavy chain so that the mutated FX polypeptide constitutes a chimeric thrombin-cleavable derivative of factor X (as described in WO2010070137). As used herein, the term “fibrinopeptide A” has its general meaning in the art and refers to a small peptide of 16 amino acid residues removed from the N-terminal segment of the a-chain of fibrinogen by the action of thrombin. The amino acid sequence of the human fibrinopeptide A is provided by SEQ ID NO:2.

According to the invention, the mutated FX polypeptide of the invention is produced by conventional automated peptide synthesis methods or by recombinant expression. General principles for designing and making proteins are well known to those of skill in the art. The mutated FX polypeptides of the invention may be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols as described in Stewart and Young; Tam et al., 1983; Merrifield, 1986 and Barany and Merrifield, Gross and Meienhofer, 1979. The mutated FX polypeptides of the invention may also be synthesized by solid-phase technology employing an exemplary peptide synthesizer such as a Model 433A from Applied Biosystems Inc. The purity of any given protein; generated through automated peptide synthesis or through recombinant methods may be determined using reverse phase HPLC analysis. Chemical authenticity of each peptide may be established by any method well known to those of skill in the art. As an alternative to automated peptide synthesis, recombinant DNA technology may be employed wherein a nucleotide sequence which encodes a protein of choice is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression as described herein below. Recombinant methods are especially preferred for producing longer polypeptides. A variety of expression vector/host systems may be utilized to contain and express the peptide or protein coding sequence. These include but are not limited to microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid or cosmid DNA expression vectors; yeast transformed with yeast expression vectors (Giga-Hama et al., 1999); insect cell systems infected with virus expression vectors (e.g., baculovirus, see Ghosh et al., 2002); plant cell systems transfected with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with bacterial expression vectors (e.g., Ti or pBR322 plasmid; see e.g., Babe et al., 2000); or animal cell systems. Those of skill in the art are aware of various techniques for optimizing mammalian expression of proteins, see e.g., Kaufman, 2000; Colosimo et al., 2000. Mammalian cells that are useful in recombinant protein productions include but are not limited to VERO cells, HeLa cells, Chinese hamster ovary (CHO) cell lines, COS cells (such as COS-7), W138, BHK, HepG2, 3T3, RIN, MDCK, A549, PC12, K562 and 293 cells. Exemplary protocols for the recombinant expression of the peptide substrates or fusion polypeptides in bacteria, yeast and other invertebrates are known to those of skill in the art and a briefly described herein below. Mammalian host systems for the expression of recombinant proteins also are well known to those of skill in the art. Host cell strains may be chosen for a particular ability to process the expressed protein or produce certain post-translation modifications that will be useful in providing protein activity. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation. Post-translational processing which cleaves a “prepro” form of the protein may also be important for correct insertion, folding and/or function. Different host cells such as CHO, HeLa, MDCK, 293, WI38, and the like have specific cellular machinery and characteristic mechanisms for such post-translational activities and may be chosen to ensure the correct modification and processing of the introduced, foreign protein.

In some embodiments, it is contemplated that the mutated FX polypeptides of the invention used in the therapeutic methods of the present invention may be modified in order to improve their therapeutic efficacy. Such modification of therapeutic compounds may be used to decrease toxicity, increase circulatory time, or modify biodistribution. For example, the toxicity of potentially important therapeutic compounds can be decreased significantly by combination with a variety of drug carrier vehicles that modify biodistribution. A strategy for improving drug viability is the utilization of water-soluble polymers. Various water-soluble polymers have been shown to modify biodistribution, improve the mode of cellular uptake, change the permeability through physiological barriers; and modify the rate of clearance from the body. To achieve either a targeting or sustained-release effect, water-soluble polymers have been synthesized that contain drug moieties as terminal groups, as part of the backbone, or as pendent groups on the polymer chain. Polyethylene glycol (PEG) has been widely used as a drug carrier, given its high degree of biocompatibility and ease of modification. Attachment to various drugs, proteins, and liposomes has been shown to improve residence time and decrease toxicity. PEG can be coupled to active agents through the hydroxyl groups at the ends of the chain and via other chemical methods; however, PEG itself is limited to at most two active agents per molecule. In a different approach, copolymers of PEG and amino acids were explored as novel biomaterials which would retain the biocompatibility properties of PEG, but which would have the added advantage of numerous attachment points per molecule (providing greater drug loading), and which could be synthetically designed to suit a variety of applications.

A further object of the present invention relates to a nucleic acid molecule which encodes for a mutated FX polypeptide of the present invention.

As used herein, the term “nucleic acid molecule” has its general meaning in the art and refers to a DNA or RNA molecule. However, the term captures sequences that include any of the known base analogues of DNA and RNA such as, but not limited to 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5- methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyamino-methyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, -uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.

In some embodiments, the nucleic acid molecule of the present invention is included in a suitable vector, such as a plasmid, cosmid, episome, artificial chromosome, phage or a viral vector. So, a further object of the invention relates to a vector comprising a nucleic acid encoding for a mutated FX polypeptide of the invention. Typically, the vector is a viral vector which is an adeno-associated virus (AAV), a retrovirus, bovine papilloma virus, an adenovirus vector, a lentiviral vector, a vaccinia virus, a polyoma virus, or an infective virus. In some embodiments, the vector is an AAV vector. As used herein, the term “AAV vector” means a vector derived from an adeno- associated virus serotype, including without limitation, AAV1, AAV2, AAV3, AAV4, AAVS, AAV6, AAV7, AAV8, AAV9, and mutated forms thereof AAV vectors can have one or more of the AAV wild-type genes deleted in whole or part, preferably the rep and/or cap genes, but retain functional flanking ITR sequences. Retroviruses may be chosen as gene delivery vectors due to their ability to integrate their genes into the host genome, transferring a large amount of foreign genetic material, infecting a broad spectrum of species and cell types and for being packaged in special cell- lines. In order to construct a retroviral vector, a nucleic acid encoding a gene of interest is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective. In order to produce virions, a packaging cell line is constructed containing the gag, pol, and/or env genes but without the LTR and/or packaging components. When a recombinant plasmid containing a cDNA, together with the retroviral LTR and packaging sequences is introduced into this cell line (by calcium phosphate precipitation for example), the packaging sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media. The media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. Lentiviruses are complex retroviruses, which, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural function. The higher complexity enables the virus to modulate its life cycle, as in the course of latent infection. Some examples of lentivirus include the Human Immunodeficiency Viruses (HIV 1, HIV 2) and the Simian Immunodeficiency Virus (SIV). Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu and nef are deleted making the vector biologically safe. Lentiviral vectors are known in the art, see, e.g.. U.S. Pat. Nos. 6,013,516 and 5,994,136, both of which are incorporated herein by reference. In general, the vectors are plasmid-based or virus-based, and are configured to carry the essential sequences for incorporating foreign nucleic acid, for selection and for transfer of the nucleic acid into a host cell. The gag, pol and env genes of the vectors of interest also are known in the art. Thus, the relevant genes are cloned into the selected vector and then used to transform the target cell of interest. Recombinant lentivirus capable of infecting a non-dividing cell wherein a suitable host cell is transfected with two or more vectors carrying the packaging functions, namely gag, pol and env, as well as rev and tat is described in U.S. Pat. No. 5,994,136, incorporated herein by reference. This describes a first vector that can provide a nucleic acid encoding a viral gag and a pol gene and another vector that can provide a nucleic acid encoding a viral env to produce a packaging cell. Introducing a vector providing a heterologous gene into that packaging cell yields a producer cell which releases infectious viral particles carrying the foreign gene of interest. The env preferably is an amphotropic envelope protein which allows transduction of cells of human and other species. Typically, the nucleic acid molecule or the vector of the present invention include “control sequences'”, which refers collectively to promoter sequences, polyadenylation signals, transcription termination sequences, upstream regulatory domains, origins of replication, internal ribosome entry sites (“IRES”), enhancers, and the like, which collectively provide for the replication, transcription and translation of a coding sequence in a recipient cell. Not all of these control sequences need always be present so long as the selected coding sequence is capable of being replicated, transcribed and translated in an appropriate host cell. Another nucleic acid sequence, is a “promoter” sequence, which is used herein in its ordinary sense to refer to a nucleotide region comprising a DNA regulatory sequence, wherein the regulatory sequence is derived from a gene which is capable of binding RNA polymerase and initiating transcription of a downstream (3′-direction) coding sequence. Transcription promoters can include “inducible promoters” (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), “repressible promoters” (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), and “constitutive promoters”.

A further object of the present invention relates to a host cell transformed with the nucleic acid molecule of the present invention. The term “transformation” means the introduction of a “foreign” (i.e. extrinsic or extracellular) gene, DNA or RNA sequence to a host cell, so that the host cell will express the introduced gene or sequence to produce a desired substance, typically a protein or enzyme coded by the introduced gene or sequence. A host cell that receives and expresses introduced DNA or RNA has been “transformed”. In a particular embodiment, for expressing and producing the mutated FX polypeptides of the present invention, prokaryotic cells, in particular E. coli cells, will be chosen. Actually, according to the invention, it is not mandatory to produce the mutated FX polypeptides of the present invention in a eukaryotic context that will favour post-translational modifications (e.g. glycosylation). Furthermore, prokaryotic cells have the advantages to produce protein in large amounts. If a eukaryotic context is needed, yeasts (e.g. saccharomyces strains) may be particularly suitable since they allow production of large amounts of proteins. Otherwise, typical eukaryotic cell lines such as CHO, BHK-21, COS-7, C127, PER.C6, YB2/0 or HEK293 could be used, for their ability to process to the right post-translational modifications of the mutated FX polypeptides of the present invention. The construction of expression vectors in accordance with the invention, and the transformation of the host cells can be carried out using conventional molecular biology techniques. The mutated FX polypeptide of the invention, can, for example, be obtained by culturing genetically transformed cells in accordance with the invention and recovering the mutated FX polypeptide expressed by said cell, from the culture. They may then, if necessary, be purified by conventional procedures, known in themselves to those skilled in the art, for example by fractional precipitation, in particular ammonium sulfate precipitation, electrophoresis, gel filtration, affinity chromatography, etc. In particular, conventional methods for preparing and purifying recombinant proteins may be used for producing the proteins in accordance with the invention.

The mutated FX polypeptides of the present invention and nucleic acid molecules encoding thereof are typically used as medicament. In particular, the nucleic acid molecules of the present invention (inserted or not into a vector) are particularly suitable for gene therapy. In some embodiments, the mutated FX polypeptides of the present invention and nucleic acid molecules (inserted or not into a vector) are particularly suitable for the treatment of haemophilia. Haemophilia includes haemophilias A or B, which may or may not be complicated by the presence of inhibitors (neutralizing allo-antibodies directed against the factor VIII or IX conventionally used for treatment); they may also be acquired haemophilias resulting from the appearance of auto antibodies associated with another pathology (autoimmune disease, cancer, lymphoproliferative syndrome, idiopathic disorder, etc.).

Accordingly a further object of the present invention relates to a method for treating haemophilia in a subject in need thereof comprising administering the subject with a therapeutically effective amount of a mutated FX polypeptide of the present invention or a nucleic acid molecule of the present invention which is inserted or not in to a vector as above described.

As used herein, the term “treatment” or “treat” refer to both prophylactic or preventive treatment as well as curative or disease modifying treatment, including treatment of patient at risk of contracting the disease or suspected to have contracted the disease as well as patients who are ill or have been diagnosed as suffering from a disease or medical condition, and includes suppression of clinical relapse. The treatment may be administered to a subject having a medical disorder or who ultimately may acquire the disorder, in order to prevent, cure, delay the onset of, reduce the severity of, or ameliorate one or more symptoms of a disorder or recurring disorder, or in order to prolong the survival of a subject beyond that expected in the absence of such treatment. By “therapeutic regimen” is meant the pattern of treatment of an illness, e.g., the pattern of dosing used during therapy. A therapeutic regimen may include an induction regimen and a maintenance regimen. The phrase “induction regimen” or “induction period” refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the initial treatment of a disease. The general goal of an induction regimen is to provide a high level of drug to a patient during the initial period of a treatment regimen. An induction regimen may employ (in part or in whole) a “loading regimen”, which may include administering a greater dose of the drug than a physician would employ during a maintenance regimen, administering a drug more frequently than a physician would administer the drug during a maintenance regimen, or both. The phrase “maintenance regimen” or “maintenance period” refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the maintenance of a patient during treatment of an illness, e.g., to keep the patient in remission for long periods of time (months or years). A maintenance regimen may employ continuous therapy (e.g., administering a drug at a regular intervals, e.g., weekly, monthly, yearly, etc.) or intermittent therapy (e.g., interrupted treatment, intermittent treatment, treatment at relapse, or treatment upon achievement of a particular predetermined criteria [e.g., disease manifestation, etc.]).

By a “therapeutically effective amount” is meant a sufficient amount of the mutated FX polypeptide or the nucleic acid molecule encoding thereof to prevent for use in a method for the treatment of the disease (e.g. haemophilia) at a reasonable benefit/risk ratio applicable to any medical treatment. It will be understood that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific polypeptide employed; and like factors well known in the medical arts. For example, it is well known within the skill of the art to start doses of the compound at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. However, the daily dosage of the products may be varied over a wide range from 0.01 to 1,000 mg per adult per day. Preferably, the compositions contain 0.01, 0.05, 0.1, 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0, 50.0, 100, 250 and 500 mg of the active ingredient for the symptomatic adjustment of the dosage to the subject to be treated. A medicament typically contains from about 0.01 mg to about 500 mg of the active ingredient, preferably from 1 mg to about 100 mg of the active ingredient. An effective amount of the drug is ordinarily supplied at a dosage level from 0.0002 mg/kg to about 20 mg/kg of body weight per day, especially from about 0.001 mg/kg to 7 mg/kg of body weight per day.

According to the invention, the mutated FX polypeptide or the nucleic acid molecule (inserted or not into a vector) of the present invention is administered to the subject in the form of a pharmaceutical composition. Typically, the mutated FX polypeptide or the nucleic acid molecule (inserted or not into a vector) of the present invention may be combined with pharmaceutically acceptable excipients, and optionally sustained-release matrices, such as biodegradable polymers, to form pharmaceutical compositions. “Pharmaceutically” or “pharmaceutically acceptable” refer to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to a mammal, especially a human, as appropriate. A pharmaceutically acceptable carrier or excipient refers to a non-toxic solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. In the pharmaceutical compositions of the present invention for oral, sublingual, subcutaneous, intramuscular, intravenous, transdermal, local or rectal administration, the active principle, alone or in combination with another active principle, can be administered in a unit administration form, as a mixture with conventional pharmaceutical supports, to animals and human beings. Suitable unit administration forms comprise oral-route forms such as tablets, gel capsules, powders, granules and oral suspensions or solutions, sublingual and buccal administration forms, aerosols, implants, subcutaneous, transdermal, topical, intraperitoneal, intramuscular, intravenous, subdermal, transdermal, intrathecal and intranasal administration forms and rectal administration forms. Typically, the pharmaceutical compositions contain vehicles which are pharmaceutically acceptable for a formulation capable of being injected. These may be in particular isotonic, sterile, saline solutions (monosodium or disodium phosphate, sodium, potassium, calcium or magnesium chloride and the like or mixtures of such salts), or dry, especially freeze-dried compositions which upon addition, depending on the case, of sterilized water or physiological saline, permit the constitution of injectable solutions. The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases, the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. Solutions comprising compounds of the invention as free base or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropyl cellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms. The mutated FX polypeptide or the nucleic acid molecule (inserted or not into a vector) of the present invention can be formulated into a composition in a neutral or salt form. Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetables oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminium monostearate and gelatin. Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with several of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the typical methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The preparation of more, or highly concentrated solutions for direct injection is also contemplated, where the use of DMSO as solvent is envisioned to result in extremely rapid penetration, delivering high concentrations of the active agents to a small tumor area. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above, but drug release capsules and the like can also be employed. For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.

The invention will be further illustrated by the following figures and examples. However, these examples and figures should not be interpreted in any way as limiting the scope of the present invention.

FIGURES

FIG. 1: Schematic representation of different parts of factor X zymogen amino acid sequence.

The pre-peptide (or signal peptide) is defined by the amino acid sequence between the positions −40 to −18 and the pro-peptide by the amino acid sequence between the positions −17 to −1. The light chain corresponds to the sequence between the amino acid positions 1 to 142 and the heavy chain between amino acid positions 195 to 448. The activation peptide (positions 143 to 194) is boxed. The numbering system used appears on the same line as the sequence and the other reference system appears in grey on the line under the sequence.

EXAMPLE

Engineering and production of recombinant FX and FX derivatives cDNAs encoding wild-type (wt)-human FX (wt-hFX), and its variants FXE215Q and FXE218Q (FIG. 1) are synthetically synthesized (Eurofins, Ebersberg Germany) and cloned in expression vectors using standard molecular biological protocols. Constructs are cloned into the pLIVE- and pNUT-plasmids for in vivo expression and in vitro expression in stably transfected in BHK-21 cells, respectively (23, 24, 25). All constructs contained a DNA sequence where the FX native signal- and pro-peptide sequences where swapped with the pro-thrombin sequences and where a sequence encoding the epitope recognized by antibody HPC4 (Roche, Meylan, France) are added at the 3′ end of the FX sequence. Stable BHK-21 cell lines producing FX or variants thereof are established as described (25) and detailed in the following section.

Obtention of Cell Lines Expressing the Recombinant Derivatives

The pNUT-constructs are transfected into Baby hamster kidney cells (BHK) using the jetPEI reactant (Qbiogen, Ozyme, France) as specified by the provider. After selection of transfected cells with medium containing methotrexate (Sigma) at a concentration of 100 μM, single clones are picked and propagated in selective medium to obtain stable cell lines. Production of factor X antigen is assayed by enzyme-linked immunosorbent assay (ELISA) using polyclonal antibodies against factor X conjugated and not with horseradish peroxidase obtained from Cederlane (Cederlane Laboratories, Burlington, Canada). Purified human plasma derived factor X (pd-FX) from Cryopep (Montepellier, France) is used as reference.

Production and Purification of Recombinant Factor X and Derivatives

Stable cell lines producing recombinant factor X, and derivatives are maintained in 300 cm2 flasks for protein production in DMEM/F-12 supplemented with 10% FCS, 50 μM methotrexate, 100 U/ml penicillin, 100 μg/ml streptomycin, and 5 μg/ml vitamin K1. Protein of interest containing medium is harvested every 48 hours. Benzamidine and PMSF are added to a final concentration of 10 and 2 mM, respectively, and the medium centrifuged (6 000 g), passed over cellulose acetate membranes (0.45 μm) to eliminate cell debris, and stored at −20° C. until use. Conditioned medium is thawed at 37° C. EDTA is added to a final concentration of 5 mM. The medium is diluted in distilled water and in Tris (pH 7.4), to bring the final Tris and NaCl concentration to 25 and 60 mM, respectively. The mixture is then stirred at room temperature for 30 min with QAE Sephadex A-50 beads to achieve a final concentration of 0.25% (wt/v). Beads are washed before elution with 50 mM Tris (pH 7.4), 500 mM NaCl, and 10 mM benzamidine. Recombinant proteins contained in the eluted fractions (ELISA) are immediately dialyzed against 25 mM Tris (pH 7.4), and 100 mM NaCl, containing 10 mM benzamidine, and stored at −20° C. before use. Concentrated proteins are thawed at 37° C. Calcium is added to a final concentration of 5 mM. Purification of recombinant proteins is performed by affinity-chromatography using HPC-4-agarose (Roche, Meylan, France) as instructed by the provider. 1 h prior to use as a zymogen, factor X derivatives are incubated with 1 mM PMSF to neutralize any trace of activated factor X that may be generated during production or purification of the recombinant protein. Control experiments indicate that after 30 min in Tris-HC1buffer, PMSF is fully hydrolyzed and does not interfere with other reactions. Protein purity is assessed using 10% SDS-polyacrylamide gel electrophoresis analysis of the recombinant proteins under reducing (100 mM dithiothreitol, final concentration) and non-reducing conditions followed by staining with Coomassie Brilliant Blue R-250. Factor X identification is carried out after the purified recombinant proteins are reduced and loaded onto a 10% SDS-polyacrylamide gel. The resolved proteins are transferred to an Immobilon membrane and blotted using polyclonal antibodies against factor X conjugated with horseradish peroxydase (Cederlane). The purified derivatives are aliquoted and stored at −80° C. until use. The concentration of the aliquot is estimated by its absorbance at 280 nm, taking 1.16 to be the extinction coefficient (E280 nm 0.1%) of factor X.

Thrombin Generation Assay

Thrombin generation is measured according to the method described by Hemker et al (26), in a Fluoroscan Ascent fluorometer (Thermolabsystems OY, Helsink, Finland) equipped with a dispenser. Briefly, 40 μl of plasma supplemented with either saline (control) or with indicated concentration of recombinant factor X derivatives are dispensed into round-bottom 96-well microtiter plates. Ten μl of a mixture containing TF (recombinant lipidated human tissue factor, Innovin®,obtained from Dade Behring) and phospholipids (PL) vesicles is added to the plasma sample to obtain a final concentration of 1 pM TF and 4 μM PL vesicles. PL vesicles prepared from L-α-Phosphatidyl-L-serine (PS) L-α-phosphatidylethanolamine (PE) and L-α-phosphatidylcholine (PC) (Avanti Polarlipids, Albaster, Ala., USA) and of nominal 100 nm-diameter (PC:PE:PS, 3:1:1) are synthesized by the method of membrane extrusion (27). Phospholipid concentration is determined by phosphate analysis. The mixture is incubated 10 minutes at 37° C. Finally, thrombin generation is triggered by adding 10 μl of starting reagent containing fluorogenic substrate and CaCl2. Fluorogenic substrate 1-1140 (Z-Gly-Gly-Arg-AMC) is from Bachem AG (Bubendorf, Switzerland). Kinetics of thrombin generation in clotting plasma is monitored for 60 min at 37° C. using a calibrated automated thrombogram and analyzed using the Thrombinoscope™ software (Thrombinoscope B.V., Maastricht, the Netherlands). Four wells are needed for each experiment, two wells to measure thrombin generation of a plasma sample and two wells for calibration. All experiments are carried out in triplicate and the mean value is reported. Endogenous thrombin potential (ETP), i.e. area under the curve, peak thrombin, and lag time for thrombin detection were determined. In some experiments, immunodepleted FVIII-plasma (Diagnostica Stago, Asnieres, France) is supplemented with FX variants (150 and 450 nM final concentrations) or is spiked with different amounts (%) of normal plasma to achieve the indicated concentrations of FVIII (0.025, 0.1, and 1 U/ml). Finally, experiments are performed using immunodepleted FIX-plasma (Diagnostica Stago, Asnieres, France).

Sequences:

SEQ ID NO: 1: Factor X (Homo sapiens) MGRPLHLVLL SASLAGLLLL GESLFIRREQ ANNILARVTR ANSFLEEMKK GHLERECMEE TCSYEEAREV FEDSDKTNEF WNKYKDGDQC ETSPCQNQGK CKDGLGEYTC TCLEGFEGKN CELFTRKLCS LDNGDCDQFC HEEQNSVVCS CARGYTLADN GKACIPTGPY PCGKQTLERR KRSVAQATSS SGEAPDSITW KPYDAADLDP TENPFDLLDF NQTQPERGDN NLTRIVGGQE CKDGECPWQA LLINEENEGF CGGTILSEFY ILTAAHCLYQ AKRFKVRVGD RNTEQEEGGE AVHEVEVVIK HNRFTKETYD FDIAVLRLKT PITFRMNVAP ACLPERDWAE STLMTQKTGI VSGFGRTHEK GRQSTRLKML EVPYVDRNSC KLSSSFIITQ NMFCAGYDTK QEDACQGDSG GPHVTRFKDT YFVTGIVSWG EGCARKGKYG IYTKVTAFLK WIDRSMKTRG LPKAKSHAPE VITSSPLK SEQ ID NO: 2: fibrinopeptide A (Homo sapiens) ADSGEGDFLA EGGGVR

Results:

Thrombin Generation in FVIII and FIX-Deficient Plasmas

The potential of different concentrations of FVIII, 1, 0.1, and 0.025 U/ml corresponding to a normal individual (control), a mild and a moderate hemophilia, respectively, to compensate for the absence of FVIII in the generation of thrombin was determined using immunodepleted FVIII-deficient human plasma. To this end, coagulation in immunodepleted FVIII-deficient human plasma, spiked with different amounts (%) of normal pool plasma to achieve the desired concentration of FVIII was initiated by the addition of TF (1 pM) and phospholipids (4 μM). The same approach was used with immunodepleted FIX-deficient plasma. Relevant thrombin generation parameters such as ETP and peak thrombin generation were determined. In the absence of any added normal pool plasma, this resulted in an ETP and a peak thrombin generation relatively low (for summary see Tables 1 and 2). Both values are significantly reduced compared to normal plasma. Where the activity of the FX variant was compared to wild-type FX, it was compared to a recombinant wild-type FX polypeptide (FX-WT) that was expressed and purified using the same conditions as used for the variant FX polypeptide to ensure that any differences in activity were the result of the mutation(s), and not the result of differences in, for example, post-translational modifications associated with different expression systems. Thus, the wild-type FX polypeptide used for comparison was the recombinant wild-type FX expressed from BHK cells as a polypeptide whose amino acid sequence is set forth in SEQ ID NO:1. As expected, the addition of FX derivatives (150 and 450 nM final concentrations) resulted in enhancement of thrombin generation in FVIII-deficient plasma (Table 1) with both ETP and peak thrombin generation being within the same range as found for normal plasma (Table 2). A similar improvement of the coagulation defect was observed when tested in immunodepleted FIX-deficient plasma (Table). Furthermore, no correction of thrombin generation was observed by the addition of wt-FX up to the highest concentration tested (450 nM). These data indicate that under the conditions employed, the presence of the mutation gives the capacity to FX to overcome the absence of FVIII or FIX for efficient thrombin generation.

Tables:

TABLE 1 Thrombin generation test in FVIII-deficient plasma (Cryopep, Montpellier). Parameters for measuring thrombin generation (ETP, thrombin peak) were measured in immunodepleted FVIII-deficient plasma in the presence of tissue factor (1 pM) and phospholipids (4 μM) with or without FVIII or FXE401Q. Data are presented as mean ± SD. Added coagulation factor in FVIII-deficient ETP Thromin plasma n (nM · min) Peak (nM) FVIII (1 U/ml) 3 1267 ± 182 293 ± 38 FVIII (0.1 U/ml) 3 908 ± 92 125 ± 44 FVIII (0.025 U/ml) 3 724 ± 87  60 ± 17 None 3 460 ± 38 25 ± 4 FXE401Q (450 nM) 3 1202 ± 234  99 ± 15 FXE401Q (150 nM) 3  990 ± 176  61 ± 14

TABLE 2 Thrombin generation test in FIX-immunodepleted plasma (Stago, France). Parameters for measuring thrombin generation (ETP, thrombin peak) were measured in immunodepleted FIX- deficient plasma in the presence of tissue factor (1 pM) and phospholipids (4 μM) with or without FVIII or FXE401Q. Data are presented as mean ± SD Added coagulation factor in FIX-deficient ETP Thromin plasma n (nM · min) Peak (nM) FIX (1 U/ml) 3 1038 ± 88  238 ± 30 FIX (0.1 U/ml) 3 388 ± 83 25 ± 5 FIX (0.025 U/ml) 3 198 ± 28 10 ± 2 None 3 141 ± 32  6 ± 2 FXE401Q (450 nM) 3 1371 ± 440  94 ± 18 FXE401Q (150 nM) 3 1068 ± 523  52 ± 21

REFERENCES

Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.

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1-6. (canceled)
 7. A nucleic acid molecule which encodes for a mammalian the mutated factor X polypeptide having a sequence identity as set forth in SEQ ID NO:1, which comprises a heavy chain wherein at least one amino acid residue at position 441 and/or position 448, wherein said factor X polypeptide is not inactivated by a factor X inhibitor selected from the group consisting of antithrombin (AT), tissue pathway inhibitor (TFPI) and alloantibodies to factor X.
 8. A vector which comprises the nucleic acid molecule of claim
 7. 9. The vector of claim 8 wherein the vector is an AAV vector.
 10. A host cell which is transformed with the nucleic acid molecule of claim 7 or a vector comprising the nucleic acid molecule.
 11. (canceled)
 12. A method of treating haemophilia in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a mammalian mutated factor X polypeptide having a sequence identity as set forth in SEQ ID NO:1, which comprises a heavy chain wherein at least one amino acid residue at position 441 and/or position 448, wherein said factor X polypeptide is not inactivated by a factor X inhibitor selected from the group consisting of antithrombin (AT), tissue pathway inhibitor (TFPI) and alloantibodies to factor X or a nucleic acid encoding the mammalian mutated factor X polypeptide.
 13. (canceled)
 14. The method of claim 12, wherein the nucleic acid is present in a vector.
 15. The method of claim 12, wherein the nucleic acid is not present in a vector. 